If you're sure it's not carpal tunnel, could it be coming from your elbow or neck? There are two nerves that could be yelling in the thumb. Musculocutaneous is the biggie, and some folks have radial nerve doing sensory business on just a tiny bit of the base of the thumb almost at the wrist. The whole "which nerve goes where" thingy with arms and hands totally confuses me. Usually it's median nerve that causes the most trouble with carpal tunnel.
You can do a quick screening of your carpal tunnel (just to see if it's crowded in there) by putting the backs of your hands together in front of you with fingers pointing downward (like an inside-out and upside-down "prayer"). Hold that position for a minute. If you get tingling/burning/pain/ouchies/irritation, then something in your carpal tunnel is unhappy. That's called a Phalen's Test, and really doesn't tell you much but could give you an idea.
There are a huge number of things (some of them pretty weird) that can cause carpal tunnel syndrome. ANYTHING that's messing with your hands should be checked out by a doc/hand therapist/OT. Hands are precious!
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